tbuckley/cabot-search huggingface dataset:
Abstract 5647: PTEN loss is associated with elevation of cell cycle signature in human glioblastoma transcriptome
Authors: Tian Liu, Penelope Mei-Yu Or, Chi-Wai Wong, Stanley Kwok-Kuen Cheung, Yubing Wang, Yiwei Wang, Wayne Lut-Heng Ho, Andrew M. Chan
Journal: Cancer Research (2022)

Abstract Glioblastoma is the most lethal type of brain cancer with universally poor prognosis. Despite advanced treatment, the cancer recurs frequently. Phosphatase and tensin homolog (PTEN) is a tumor suppressor gene whose mutations have been found to be one of the most frequent events in GBM. PTEN acts as a negative regulator of the phosphoinositide 3-kinase (PI3K) pathway. GBM transcriptome data from The Cancer Genome Atlas (TCGA) revealed a positive enrichment of cell cycle and PI3K pathway. Moreover, weighted gene co-expression network analysis (WGCNA) on TCGA GBMLGG cohort revealed a cell cycle-related module (‘cell-cycle’ module), which was shown to be positively correlated with PTEN mutation status. This ‘cell-cycle’ module also showed a positive correlation with glioma aggressiveness.We then utilized a nestin-cre;Pten-fl/fl mouse model to investigate the consequences of PTEN loss that may be involved in GBM. Based on our preliminary data, transcriptomic profiling of primary astrocytes derived from Pten knockout mice revealed an overlapping enrichment of cell cycle related pathways with human GBM. Four cell cycle genes, RCC1, RCC2, NEK2, and CHK2, were validated to be significantly upregulated in Pten-null astrocytes by qRT-PCR. Regulator of chromatin condensation 1 (RCC1) and Regulator of chromatin condensation 2 (RCC2) both belong to the RCC1 family. Accumulating evidence demonstrated that both RCC1 and RCC2 are involved in tumorigenesis of multiple cancers and cell cycle progression. By siRNA inhibition, we demonstrated that silencing of either RCC1 or RCC2 in glioblastoma cell lines suppresses GBM cell growth. Moreover, we found that RCC2 is essential for both G1-S and G2-M transition. Additionally, RCC2 silencing and a PI3K inhibitor LY294002 inhibit glioblastoma cell viability in a synergistic manner. In summary, PTEN deficiency leads to the alteration of cell cycle progression, which may promote tumorigenesis of glioblastoma. RCC1 and RCC2 have been demonstrated to be potential targets regulated by PTEN and affects cell viability. RCC2 was shown to be a key regulator of cell cycle progression. To further explore the RCC1 and RCC2 roles, we will find the potential downstream target of RCC1 and RCC2 and its potential therapeutic effect in vivo. Funding: This work is supported by a General Research Fund grant (#14113519) from the University Grants Committee of Hong Kong. Citation Format: Tian Liu, Penelope Mei-Yu Or, Chi-Wai Wong, Stanley Kwok-Kuen Cheung, Yubing Wang, Yiwei Wang, Wayne Lut-Heng Ho, Andrew M. Chan. PTEN loss is associated with elevation of cell cycle signature in human glioblastoma transcriptome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5647.
Abstract 5125: Biological and clinical value of OCT4A/SPP1C axis in endometrial and lung adenocarcinoma
Authors: Kyohei Irie, Nobuhiko Mizuno, Tomoyuki Miyamoto, Aiji Ohtsuka, Hiromasa Yamamoto, Shinichi Toyooka, Hisashi Masuyama, Mitsuko Kosaka
Journal: Cancer Research (2022)

Abstract Background: It is largely unclear whether octamer-binding transcription factor 4A (OCT4A, OCT3/4A) functions physiologically or pathologically in adult somatic tissues and related cancers. We have recently identified OCT4A translation in a human cancer cell subpopulation that might exacerbate cell migration and invasion. Here, we focus on biological and clinical features of OCT4A and its relationship with secreted phosphoprotein 1(SPP1), which is strongly related to the malignant progression of numerous tumors. Methods: RT-PCR or qPCR analysis was used to identify full-length spliced forms of OCT4A and SPP1 transcripts in non-tumor and tumor human cells. An OCT4A-FLAG-tagged genomic transgene identified OCT4A-positive cancer cells. Cell-ablation of OCT4A-positive cells using promoter-driven diphtheria toxin A was used to examine the potential role of OCT4A in lung and endometrial adenocarcinoma cells. OCT4A and SPP1 transcripts in early-stage lung adenocarcinoma (stage I, fifty-eight cases) were analyzed and compared with pathohistological and prognostic features. Results: We found that OCT4A and SPP1C are co-expressed in highly aggressive human lung and endometrial adenocarcinoma cell lines but not in mesothelioma or non-tumor cell lines. Ablation of OCT4A-positive cells significantly decreased cancer-cell migration and SPP1C mRNA levels. The OCT4A/SPP1C axis was found in primary, early-stage, lung adenocarcinomas, and all four cases of recurrence and/or metastasis out of 58 cases were included in the OCT4A and SPP1C positive group. Conclusions: Co-expression of OCT4A and SPP1C may correlate with human cancer cell migration and the OCT4A/SPP1C axis may have a prognostic value in high-risk, early-stage lung adenocarcinomas. References: Stem Cells (2018), 36:1341-54. BMC Cancer (2020), 20:521. Gene expression of OCT4A and SPP1 variants in 58 cases of early-stage lung adenocarcinoma OCT4A(-) OCT4A(+) OCT4A(++) SPP1A(+),SPP1C(+) 0 cases 9 cases 17cases(including 4 cases of recurrence or metastasis ) SPP1A(+),SPP1C(-) 3 cases 6 cases 7 cases SPP1A(-),SPP1C(-) 13cases 3 cases 0 cases Citation Format: Kyohei Irie, Nobuhiko Mizuno, Tomoyuki Miyamoto, Aiji Ohtsuka, Hiromasa Yamamoto, Shinichi Toyooka, Hisashi Masuyama, Mitsuko Kosaka. Biological and clinical value of OCT4A/SPP1C axis in endometrial and lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5125.
Abstract LB527: A novel dimeric small molecule-radio conjugate targeting fibroblast activation protein with high and prolonged tumor uptake
Authors: Samuele Cazzamalli, Andrea Galbiati, Aureliano Zana, Matilde Bocci, Jacopo Millul, Jacqueline Mock, Abdullah Elsayed, Dario Neri
Journal: Cancer Research (2022)

Abstract Imaging procedures based on small molecule-radio conjugates targeting Fibroblast Activation Protein (FAP) are taking the spotlight in clinical practice for the diagnosis of a wide variety of cancer lesions. However, therapeutic applications of FAP-targeting radioligand therapeutics are limited by their short residence time in tumor lesions. We have recently described the discovery of OncoFAP, a novel ultra-high affinity ligand of FAP which has been already validated for PET imaging applications in more than twenty patients with solid tumors. In this abstract, we describe the development and in vivo characterization of BiOncoFAP, a dimeric FAP targeting small molecule based on OncoFAP. In particular, OncoFAP and BiOncoFAP displayed a superimposable affinity for recombinant human FAP (KD = 970 pM and 993 pM, respectively, measured by Fluorescence Polarization). Moreover, the two ligands exhibited a clear selectivity for the target, without significantly interacting with a wide panel of non-target proteins. BiOncoFAP was coupled to a DOTAGA chelator, suitable for radiolabeling with [177Lu]Lu for therapeutic applications. Cold [natLu]Lu-BiOncoFAP-DOTAGA showed an excellent stability in both mouse and human serum, with half-life longer than 5 days, supporting in vivo investigations. In a head-to-head in vivo biodistribution comparative study against [177Lu]Lu-OncoFAP-DOTAGA, [177Lu]Lu-BiOncoFAP-DOTAGA exhibited a more stable and prolonged residence time in FAP-positive tumors implanted in immunodeficient mice (~20% ID/g and ~200-to-1 tumor-to-blood ratio, 24 h after systemic administration). Notably, [177Lu]Lu-BiOncoFAP-DOTAGA did not significantly accumulate in healthy organs, thus showing an outstanding tumor-to-organ ratio (e.g., 12-to-1 tumor-to-kidney and 34-to-1 tumor-to-liver ratio, at the 24 h time point). These findings heighten BiOncoFAP as promising candidate for the development of anti-cancer radioligand therapeutics towards FAP-expressing tumor lesions. Citation Format: Samuele Cazzamalli, Andrea Galbiati, Aureliano Zana, Matilde Bocci, Jacopo Millul, Jacqueline Mock, Abdullah Elsayed, Dario Neri. A novel dimeric small molecule-radio conjugate targeting fibroblast activation protein with high and prolonged tumor uptake [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB527.
The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota
Authors: Joseph Stevens, Shelby Steinmeyer, Madeline Bonfield, Laura Peterson, Timothy Wang, Jerilyn Gray, Ian Lewkowich, Yan Xu, Yina Du, Minzhe Guo, James L. Wynn, William Zacharias, Nathan Salomonis, Lisa Miller, Claire Chougnet, Dennis Hartigan O’Connor, Hitesh Deshmukh
Journal: Science Translational Medicine (2022)

Although modern clinical practices such as cesarean sections and perinatal antibiotics have improved infant survival, treatment with broad-spectrum antibiotics alters intestinal microbiota and causes dysbiosis. Infants exposed to perinatal antibiotics have an increased likelihood of life-threatening infections, including pneumonia. Here, we investigated how the gut microbiota sculpt pulmonary immune responses, promoting recovery and resolution of infection in newborn rhesus macaques. Early-life antibiotic exposure interrupted the maturation of intestinal commensal bacteria and disrupted the developmental trajectory of the pulmonary immune system, as assessed by single-cell proteomic and transcriptomic analyses. Early-life antibiotic exposure rendered newborn macaques more susceptible to bacterial pneumonia, concurrent with increases in neutrophil senescence and hyperinflammation, broad inflammatory cytokine signaling, and macrophage dysfunction. This pathogenic reprogramming of pulmonary immunity was further reflected by a hyperinflammatory signature in all pulmonary immune cell subsets coupled with a global loss of tissue-protective, homeostatic pathways in the lungs of dysbiotic newborns. Fecal microbiota transfer was associated with partial correction of the broad immune maladaptations and protection against severe pneumonia. These data demonstrate the importance of intestinal microbiota in programming pulmonary immunity and support the idea that gut microbiota promote the balance between pathways driving tissue repair and inflammatory responses associated with clinical recovery from infection in infants. Our results highlight a potential role for microbial transfer for immune support in these at-risk infants.
Abstract 1925: Ovarian tumor diagnosis using deep convolutional neural networks and denoising convolutional autoencoder
Authors: Youn Jin Choi, Yuyeon Jung
Journal: Cancer Research (2022)

Abstract Objective: Discrimination of ovarian tumors is a necessary procedure for proper treatment. In this study, we developed a convolutional neural network model with a convolutional autoencoder (CNN-CAE) to classify ovarian tumors. Methods: A total of 1,613 ultrasound images of ovarian tumors with the known pathologic diagnosis were pre-processed and augmented for deep learning analysis. We designed the CNN-CAE model that removes the unnecessary information on ultrasound images (e.g. calipers and annotations) and classifies ovarian tumors into five classes. We assessed the CNN-CAE model performance using a validation set of 327 images with the following metrics: accuracy, sensitivity, specificity, and the area under the receiver operating characteristic curve (AUC). Gradient-weighted class activation mapping (Grad-CAM) was applied to visualize and verify the CNN-CAE model results qualitatively. Results: In classifying normal versus ovarian tumors, the CNN-CAE model showed 96.0% accuracy, 96.5% sensitivity, and 0.9837 AUC with DenseNet161 CNN architecture. In determining malignancy of ovarian tumors, the CNN-CAE model showed 86.85% accuracy, 75.68% sensitivity, and 0.9225 AUC with DenseNet121 CNN architecture. The Grad-CAM results show that the CNN-CAE model finds valid texture and morphology features from the ultrasound images and classifies ovarian tumors from these features. Conclusion: CNN-CAE is a feasible diagnostic tool that is capable of robustly classifying ovarian tumors by eliminating marks on ultrasound images. CNN-CAE demonstrates a significant application value in clinical conditions. Citation Format: Youn Jin Choi, Yuyeon Jung. Ovarian tumor diagnosis using deep convolutional neural networks and denoising convolutional autoencoder [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1925.
Abstract 3330: GB5121 is a novel highly potent and selective CNS-penetrant BTK inhibitor for CNS malignancies
Authors: Isharat Yusuf, Sunil Sahdeo, Taylor Ismaili, Zachary Naiman, David Guimond, Theodore Schiff, Bryan Clemons, Krystal Herman, Bryanna Paulson, Kay Hou, Kristen Taylor Meadows, Michael Kennedy, Mark Rose, Laura Carter
Journal: Cancer Research (2022)

Abstract Inhibitors of Bruton’s tyrosine kinase (BTK) are approved treatments for several B cell lymphomas. However, they are characterized by modest selectivity and/or limited central nervous system (CNS) penetrance in instances of CNS disease. GB5121 is an orally available, selective, irreversible small molecule BTK inhibitor. GB5121 was selected based on its potency, specificity, and high brain penetrance in preclinical models. We evaluated its pharmacodynamic properties using both cell-free enzymatic and cell-based functional assays, showing covalent BTK inactivation with a potency in the nM range. GB5121 furthermore demonstrated rapid BTK inactivation kinetics (Kinact/Ki) in both peripheral and CNS tissue, a critical parameter for covalent irreversible inhibitors. In a kinome scan, GB5121 exhibited high kinase selectivity against 349 kinases with only TEC/TXK demonstrating &amp;gt;50% inhibition at 1 µM; GB5121 did not inhibit phosphorylation of EGFR in a cell-based assay. When compared with other BTK inhibitors, GB5121 showed superior CNS target occupancy using a probe-based ELISA measuring free BTK in the brain of mice receiving 3 daily oral doses of 10 mg/kg. GB5121 also demonstrated significantly higher brain to plasma ratio in mice with an intact blood brain barrier. Specifically, GB5121 showed ~2-fold higher brain concentrations with lower plasma levels than ibrutinib. In non-human primates, a 1:1 brain to plasma concentration ratio was demonstrated for GB5121 for up to 8 hours with both oral (30 mg/kg) and IV (2 mg/kg) doses. Together, these features differentiate GB5121 from both FDA-approved BTK inhibitors as well as those currently under clinical investigation. Our data supports the use of GB5121 in clinical trials where BTK is a known driver of malignancies, including in CNS lymphoma. Citation Format: Isharat Yusuf, Sunil Sahdeo, Taylor Ismaili, Zachary Naiman, David Guimond, Theodore Schiff, Bryan Clemons, Krystal Herman, Bryanna Paulson, Kay Hou, Kristen Taylor Meadows, Michael Kennedy, Mark Rose, Laura Carter. GB5121 is a novel highly potent and selective CNS-penetrant BTK inhibitor for CNS malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3330.
Abstract LB534: Development of GB2101, a novel anti-CCR8 antibody for cancer treatment
Authors: Qinglin Du, Yiqi Cao, Xueyan Yang, Jing Lu, Fei Peng, Wenming Zhou, Liwen Liang, James Li, Shuhua Han
Journal: Cancer Research (2022)

Abstract Background: Regulatory T cells (Tregs) play a crucial role in suppressing immune response and maintaining hemostasis and immune tolerance. Tregs are enriched in the tumor microenvironment (TME) and suppress anti-tumor immunity. Therefore, specific depletion of Tregs in the TME is expected to reduce anti-tumor immune suppression without affecting hemostasis in the periphery. The C-C motif chemokine receptor 8 (CCR8), highly expressed on Tregs from TME but significantly lower expressed on Tregs from peripheral blood, provides an ideal target for preferentially deletion of Tregs within tumors. GB2101 is a novel anti-CCR8 monoclonal antibody generated from hybridoma. The data from in vitro and in vivo studies indicated that GB2101 is a good PCC molecule with great potential for clinical development. Methods: GB2101 was generated by immunization of CCR8 gene plus CCR8 over-expressing cells in mice followed by hybridoma technology. The binding of the antibody to CCR8-expressing cells was detected by flow cytometry. CCL1 ligand blocking was assessed by flow cytometry and calcium flux assay. Antibody-dependent cell-mediated cytotoxicity (ADCC) function was evaluated by Jurkat-CD16A-NFAT reporter system. In vivo anti-tumor efficacy was assessed in syngeneic model using human CCR8 knock-in mice. Results: GB2101 displayed potent binding to cells expressing CCR8. GB2101 efficiently blocked CCL1 binding and CCL1-induced signals in CCR8 expressing cells. ADCC activity against target cells was observed and afucosylated version of GB2101 improved ADCC response. GB2101 significantly inhibited tumor growth in syngeneic model. Conclusions: GB2101 is a novel monoclonal antibody specifically binding to CCR8 with high affinity, and efficiently blocked CCL1-CCR8 pathway and suppressed tumor growth in vivo. Therefore, it is a very promising preclinical candidate that may be used in the treatment of multiple tumor types. Citation Format: Qinglin Du, Yiqi Cao, Xueyan Yang, Jing Lu, Fei Peng, Wenming Zhou, Liwen Liang, James Li, Shuhua Han. Development of GB2101, a novel anti-CCR8 antibody for cancer treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB534.
Abstract 787: RE1-silencing transcription factor (REST) controls neuroendocrine gene programs in pancreatic ductal adenocarcinoma
Authors: Kevin Alexander MacPherson, Meghan M. Joly, Brittany Allen-Petersen, Carl Pelz, Mary C. Thoma, Kristof Torkenczy, Andrew Adey, Daniel Liefwalker, Patrick J. Worth, Rosalie C. Sears
Journal: Cancer Research (2022)

Abstract Neuroendocrine (NE) differentiation features contribute to intratumoral heterogeneity and aggressive biology in a subset of pancreatic ductal adenocarcinoma (PDAC) tumors associated with poor disease outcome. We recently showed that treating pancreatic cancer cells with gemcitabine, a standard-of-care chemotherapy for PDAC, increases expression of NE markers, suggesting that ductal to neuroendocrine lineage plasticity could play a role in drug resistance. NE features in prostate cancer have been previously associated with loss of the neuronal gene repressor RE1-Silencing Transcription Factor (REST); in the present study, we explore a potential role of REST in regulating NE differentiation in PDAC. Our experiments show that loss of REST in PDAC cells increases NE gene expression, gemcitabine resistance, and colony formation. RNA sequencing data from gemcitabine-treated PDAC cells were enriched for REST target genes, suggesting gemcitabine relieves REST-mediated repression. Chromatin immunoprecipitation experiments corroborated this by demonstrating that gemcitabine reduces REST binding to the NE genes SYP and SNAP25. In addition, single cell ATAC sequencing also uncovered a heterogeneous response to gemcitabine treatment, revealing two gemcitabine-driven cell states with differing REST motif accessibility. Our study indicates that REST controls NE gene programs in PDAC and that loss of REST promotes gemcitabine resistance and oncogenic growth. Mirroring the heterogeneity of PDAC tumors, a subset of PDAC cells treated with gemcitabine have reduced REST motif accessibility, which may reflect a therapy resistant NE-like subpopulation. Citation Format: Kevin Alexander MacPherson, Meghan M. Joly, Brittany Allen-Petersen, Carl Pelz, Mary C. Thoma, Kristof Torkenczy, Andrew Adey, Daniel Liefwalker, Patrick J. Worth, Rosalie C. Sears. RE1-silencing transcription factor (REST) controls neuroendocrine gene programs in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 787.
Abstract 5829: Characterizing cargoes of extracellular vesicles in promoting breast cancer growth and chemotherapy resistance
Authors: Harrison Ngue, Hyejin Kim, Shobha Vasudevan
Journal: Cancer Research (2022)

Abstract Cancer cells employ bidirectional cell communication to maintain growth and metastasis in the tumor microenvironment. One mechanism of communication that has become increasingly appreciated is the secretion of extracellular vesicles (EVs), heterogeneous multi-signal messengers that support cancer dissemination through the transfer of biomolecules such as oncoproteins and noncoding RNA species. However, little is understood about EVs in relation to chemotherapy resistance. In this study, we profiled two different breast cancer cell lines: 1) BT549 (triple negative), treated with gemcitabine and paclitaxel chemotherapy, and 2) MCF7 (estrogen receptor-positive), treated with palbociclib and fulvestrant, compared to their wild-type states. EVs were collected from these cells using tangential flow filtration and quantified with Brownian motion-based nanoparticle tracking analysis and microfluidic resistive pulse sensing, and profiling of RNA and peptide markers was completed through RT-qPCR and Western blotting, respectively. Initial data showed that representative mitochondrial ribosomal genes mt12S and MRPS14 were among the most upregulated RNAs in our drug-exposed EV samples, indicating that extracellular transfer of mitochondrial materials plays a role in cancer growth under chemotherapy stress. These findings were supported by prior genetic research at the Vasudevan laboratory, in which a set of mitochondrial ribosomal RNAs was found to be upregulated in cytosine arabinoside-induced chemoresistant acute monocytic leukemia cells, as well as by the recent discovery of mitovesicles, a novel population of EVs that originate from mitochondria. Through additional efforts to isolate further subtypes of EVs, the mechanisms by which these mitochondrial cargoes promote chemoresistant phenotypes will be uncovered. Citation Format: Harrison Ngue, Hyejin Kim, Shobha Vasudevan. Characterizing cargoes of extracellular vesicles in promoting breast cancer growth and chemotherapy resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5829.